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CZI image to more series

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Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

CZI image to more series

Postby phm » Fri Sep 23, 2016 1:34 pm

Hi,

When I open a tile series of a czi file with bio-format (5.2.2) in Fiji I got a duplicated number series. The series appear two time first one with good dimensions (2048x2048) and second with half dimensions (1014x1024).

Pḧilippe
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Re: CZI image to more series

Postby sbesson » Fri Sep 23, 2016 3:48 pm

Hi Philippe,

this behavior might be expected. As of this Pull Request, support has been added for slides stored in CZI format. This includes both the full-resolution image but also all sub-resolution images available (which is probably the case of your 1024x1024 image).

How are you initializing your reader? You might want to make sure to pass reader.setFlattenedResolutions(false) before calling setId() to ensure images at lowest resolutions will not treated as independent series but as resolutions which can be iterated over using reader.setResolution(value)?

Best,
Sebastien
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Re: CZI image to more series

Postby phm » Fri Sep 23, 2016 9:13 pm

sbesson wrote:Hi Philippe,

this behavior might be expected. As of this Pull Request, support has been added for slides stored in CZI format. This includes both the full-resolution image but also all sub-resolution images available (which is probably the case of your 1024x1024 image).

How are you initializing your reader? You might want to make sure to pass reader.setFlattenedResolutions(false) before calling setId() to ensure images at lowest resolutions will not treated as independent series but as resolutions which can be iterated over using reader.setResolution(value)?

Best,
Sebastien


Hi Sebastien,
Is there a way to do that in macro extensions ?

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Re: CZI image to more series

Postby dgault » Mon Sep 26, 2016 1:31 pm

Hi Philippe,

The option to set the flattened resolutions value is unfortunately not currently available via the ImageJ macros. I have created a card for the Bio-Formats inbox to look into potentially adding this option to the ImageJ plugin macros in the future.

https://trello.com/c/xWnT2XZC/48-imagej ... esolutions

David Gault
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